Seriously I see it as no comparison
ToS beats the living hell out of SO3 in basically every category (except maybe music)
SO3 has terrible party AI
ToS has really fantastic customizable AI
SO3 has slow repetitive battle system (sit in corner with ninja girl and hold O for 5 mins ^^;; )
ToS has really fun exciting battle system where you're always trying to set up nice combos
SO3 has a story that tries to be something hip and cool, but ends up dragging and just being utterly ridiculous to the point where between the characters and the story it may just be the worst plot I've experienced in a rpg

ToS has a standard but very enjoyable story that is executed well and keeps the game interesting
SO3 has possibly the most dull cast ever in a rpg
ToS has about 4 great characters, 4 ok characters. But the good ones in your party are really enjoyable.
ToS has great dungeon length and good fast puzzles
SO3 has long 1 hour+ dungeons with some really stupid puzzles
ToS has fantastic detailed 60fps graphics which look fantastic in both cutscenes and battle
SO3 has good non-detailed 60fps graphics which look fantastic in battle but not so hot in cutscenes
Both are around the same length (45-55 hours main game, 10-20+ hours sidequests)
Really it just comes down to ToS looks better than SO3, ToS has a more enjoyable and interesting battle system, and ToS has story and characters 100x greater than those found in SO3.
From my pile of rpgs I pegged:
SO3 8.5
ToS 9.6
All IMHO though and I know shouta will fight me like always about SO3 ^^;;